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- ItemMelt Electrowriting of Scaffolds with a Porosity Gradient to Mimic the Matrix Structure of the Human Trabecular Meshwork(New York : Cold Spring Harbor Laboratory, 2022) Włodarczyk-Biegun, Małgorzata K.; Villiou, Maria; Koch, Marcus; Muth, Christina; Wang, Peixi; Ott, Jenna; del Campo, AranzazuThe permeability of the Human Trabecular Meshwork (HTM) regulates eye pressure via a porosity gradient across its thickness modulated by stacked layers of matrix fibrils and cells. Changes in HTM porosity are associated with increases in intraocular pressure and the progress of diseases like glaucoma. Engineered HTMs could help to understand the structure-function relation in natural tissues, and lead to new regenerative solutions. Here, melt electrowriting (MEW) is explored as a biofabrication technique to produce fibrillar, porous scaffolds that mimic the multilayer, gradient structure of native HTM. Poly(caprolactone) constructs with a height of 125-500 μm and fiber diameters of 10-12 μm are printed. Scaffolds with a tensile modulus between 5.6 and 13 MPa, and a static compression modulus in the range of 6-360 kPa are obtained by varying the scaffolds design, i.e., density and orientation of the fibers and number of stacked layers. Primary HTM cells attach to the scaffolds, proliferate, and form a confluent layer within 8-14 days, depending on the scaffold design. High cell viability and cell morphology close to that in the native tissue are observed. The present work demonstrates the utility of MEW to reconstruct complex morphological features of natural tissues.
- ItemGelation kinetics of thiol-methylsulfone (MS) hydrogel formulations for 3D cell culture(Washington, D.C. : American Chemical Society, 2022) de Miguel-Jiménez, Adrián; Ebeling, Bastian; Paez, Julieta I.; Fink-Straube, Claudia; Pearson, Samuel; del Campo, AranzazuCrosslinking chemistries that allow hydrogel formation within minutes are essential to achieve homogeneous networks and cell distributions in 3D cell culture. Thiol-methylsulfone (MS) crosslinking chemistry offers minutes-scale gelation under near-physiological conditions showing many desirable attributes for 3D cell encapsulation. Here we investigate the gelation kinetics and mechanical properties of PEG-based hydrogels formed by thiol-tetrazole methylsulfone (TzMS) crosslinking as a function of buffer, crosslinker structure, and degree of TzMS functionalization. Appropriate buffer selection ensured constant pH throughout crosslinking. The formulation containing cell adhesive ligand RGD and enzymatically-degradable peptide VPM gelled in ca. 4 min at pH 7.5, and stiffness could be increased from hundreds of Pascals to > 1 kPa by using excess VPM. The gelation times and stiffnesses for these hydrogels are highly suitable for 3D cell encapsulations, and pave the way for reliable 3D cell culture workflows in pipetting robots.
- ItemRedox-triggerable Luciferin-Bioinspired Hydrogels as Injectable and Cell-encapsulating Matrices(Washington, D.C. : American Chemical Society, 2022) Jin, Minye; Gläser, Alisa; Paez, Julieta I.Over the past few decades there has been a great interest in developing smart hydrogels that are stimuli-responsive, due to their ability to respond to variations caused by external stimuli. These materials are exploited for biomedical applications such as biosensors, injectable scaffolds, drug delivery and tissue engineering. Recently, our group reported firefly-inspired hydrogel matrices for 3D cell culture. This platform exhibited certain advantages like rapid gelation rate and tunability of mechanical and biological properties. However, this firstly reported system did not allow for fine control of the gelation onset because the crosslinking reaction started as soon as the two precursors were mixed. Moreover, one of its precursors demonstrated poor storage stability in aqueous solution. These limitations restrict its application as injectable matrices. In this article, we endow the luciferin-inspired hydrogels with redox-triggering capability, to overcome the limitations of the previous system and to widen its application range. We achieve this goal by introducing protected macromers as hydrogel polymeric precursors that can be activated in the presence of a mild reductant, to trigger gel formation in situ with high degree of control. We demonstrate that the regulation of intrinsic (e.g., structure of protecting group, reductant type) and extrinsic (e.g., pH, temperature) parameters of the triggering reaction can be used to modulate key materials properties. This novel upgraded redox-triggerable system enables precise control over gelation onset and kinetics, thus facilitating its utilization as injectable hydrogel without negatively impacting its cytocompatibility. Our findings expand the current toolkit of chemically-based stimuli-responsive hydrogels.
- ItemWorkshop on PIDs within NFDI: Report of the Working Group “Persistent Identifiers (PID)” of the Section Common Infrastructures of the NFDI(Zenodo, 2023) Arend, Daniel; Bach, Janete; Elger, Kirsten; Göller, Sandra; Hagemann-Wilholt, Stephanie; Krahl, Rolf; Lange, Matthias; Linke, David; Mayer, Desiree; Mutschke, Peter; Reimer, Lorenz; Scheidgen, Markus; Schrader, Antonia C.; Selzer, Michael; Wieder, PhilippIn order to gain an overview of the current state of the discussion on PIDs and for the identification of use cases for the initiation phase of a PID service within the NFDI basic services, the working group Persistent Identifier of the Section Common Infrastructures of the NFDI hosted an online workshop in January 2023. In the course of the workshop, members of nine different NFDI consortia presented the current application of PIDs in their consortia.
- ItemBridging the Gap Between (AI-) Services and Their Application in Research and Clinical Settings Through Interoperability: the OMI-Protocol(Hannover : Technische Informationsbibliothek, 2024-02) Sigle, Stefan; Werner, Patrick; Schweizer, Simon; Caldeira, Liliana; Hosch, René; Dyrba, Martin; Fegeler, Christian; Sigle, Stefan; Werner, Patrick; Schweizer, Simon; Caldeira, Liliana; Hosch, René; Dyrba, Martin; Fegeler, Christian; Grönke, Ana; Seletkov, Dmitrii; Kotter, Elmar; Nensa, Felix; Wehrle, Julius; Kaufmes, Kevin; Scherer, Lucas; Nolden, Marco; Boeker, Martin; Schmidt, Marvin; Pelka, Obioma; Braren, Rickmer; Stump, Shura-Roman; Graetz, Teresa; Pogarell, Tobias; Susetzky, Tobias; Wieland, Tobias; Parmar, Vicky; Wang, YuanbinArtificial Intelligence (AI) in research and clinical contexts is transforming the areas of medical and life sciences permanently. Aspects like findability, accessibility, interoperability, and reusability are often neglected for AI-based inference services. The Open Medical Inference (OMI) protocol aims to support remote inference by addressing the aforementioned aspects. Key component of the proposed protocol is an interoperable registry for remote inference services, which addresses the issue of findability for algorithms. It is complemented by information on how to invoke services remotely. Together, these components lay the basis for the implementation of distributed inference services beyond organizational borders. The OMI protocol considers prior work for aspects like data representation and transmission standards wherever possible. Based on Business Process Modeling of prototypical use cases for the service registry and common inference processes, a generic information model for remote services was inferred. Based on this model, FHIR resources were identified to represent AI-based services. The OMI protocol is first introduced using AI-services in radiology but is designed to be generalizable to other application domains as well. It provides an accessible, open specification as blueprint for the introduction and implementation of remote inference services.
- ItemA tale of two 'opens': intersections between Free and Open Source Software and Open Scholarship(Charlottesville, VA : Center for Open Science, 2020) Tennant, Jonathan P.; Agrawal, Ritwik; Baždarić, Ksenija; Brassard, David; Crick, Tom; Dunleavy, Daniel J.; Evans, Thomas Rhys; Gardner, Nicholas; Gonzalez-Marquez, Monica; Graziotin, Daniel; Greshake Tzovaras, Bastian; Gunnarson, Daniel; Havemann, Johanna; Hosseini, Mohammad; Katz, Daniel S.; Knöchelmann, Marcel; Lahti, Leo; Madan, Christopher R.; Manghi, Paolo; Marocchino, Alberto; Masuzzo, Paola; Murray-Rust, Peter; Narayanaswamy, Sanjay; Nilsonne, Gustav; Pacheco-Mendoza, Josmel; Penders, Bart; Pourret, Olivier; Rera, Michael; Samuel, John; Steiner, Tobias; Stojanovski, Jadranka; Uribe Tirado, Alejandro; Vos, Rutger; Worthington, Simon; Yarkoni, TalThere is no clear-cut boundary between Free and Open Source Software and Open Scholarship, and the histories, practices, and fundamental principles between the two remain complex. In this study, we critically appraise the intersections and differences between the two movements. Based on our thematic comparison here, we conclude several key things. First, there is substantial scope for new communities of practice to form within scholarly communities that place sharing and collaboration/open participation at their focus. Second, Both the principles and practices of FOSS can be more deeply ingrained within scholarship, asserting a balance between pragmatism and social ideology. Third, at the present, Open Scholarship risks being subverted and compromised by commercial players. Fourth, the shift and acceleration towards a system of Open Scholarship will be greatly enhanced by a concurrent shift in recognising a broader range of practices and outputs beyond traditional peer review and research articles. In order to achieve this, we propose the formulation of a new type of institutional mandate. We believe that there is substantial need for research funders to invest in sustainable open scholarly infrastructure, and the communities that support them, to avoid the capture and enclosure of key research services that would prevent optimal researcher behaviours. Such a shift could ultimately lead to a healthier scientific culture, and a system where competition is replaced by collaboration, resources (including time and people) are shared and acknowledged more efficiently, and the research becomes inherently more rigorous, verified, and reproducible.
- ItemTrain-the-Trainer Konzept zum Thema Forschungsdatenmanagement - Version 3.1(Meyrin : CERN, 2020-12-18) Biernacka, Katarzyna; Buchholz, Petra; Danker, Sarah Ann; Dolzycka, Dominika; Engelhardt, Claudia; Helbig, Kerstin; Jacob, Juliane; Neumann, Janna; Odebrecht, Carolin; Wiljes, Cord; Wuttke, UlrikeIm Rahmen des BMBF-Projekts FDMentor wurde ein deutschsprachiges Train-the-Trainer Programm zum Thema Forschungsdatenmanagement (FDM) erstellt, das nach Projektende durch Mitglieder der UAG Schulungen/Fortbildungen der DINI/nestor-AG Forschungsdaten ergänzt und aktualisiert wurde. Die behandelten Themen umfassen sowohl die Aspekte des Forschungsdatenmanagements als auch didaktische Einheiten zu Lernkonzepten, Workshopgestaltung und eine Reihe von didaktischen Methoden. Die nun veröffentlichte dritte, überarbeitete und erweiterte Version des Train-the-Trainer-Konzepts enthält Einheiten zu Methoden und Materialien für Online-Veranstaltungen. Erste Erfahrungen aus bereits online durchgeführten Train-the-Trainer-Workshops sind zusätzlich in das Konzept eingeflossen. Die mit dieser Version eingeführten didaktischen Methoden für Online-Veranstaltungen sollen die geschulten Trainer*innen dabei unterstützen, ihre Schulungsangebote auch im virtuellen Raum lebendig und interaktiv zu gestalten und dient somit auch der weitergehenden Information der bereits geschulten Teilnehmer*innen. An English version of the "Train-the-Trainer Konzept zum Forschungsdatenmanagement" is available under https://doi.org/10.5281/zenodo.4071471
- ItemLebensqualität bei Krebserkrankungen – Integration in die Versorgung (working paper von Versorgern und Betroffenen)(Hannover : Technische Informationsbibliothek, 2024) Beutter, C. N. L.; Block, N.; Berger, S.; Edo-Ferrando, P.; Heinz, B.; Läufer, K.; Lang, B.; Mächtlen, K.; Münkel, S.; Rannert, D.; Zwerenz-Kopp, F.; Fegeler, C.Im Rahmen einer Projektgruppe haben sich sowohl Versorger (ÄrztInnen, KrebsberatungsstellenmitarbeiterInnen oder PsychoonkologInnen) sowie Betroffene mit einer regulären Integration von Lebensqualitätsdaten in der Versorgung befasst. Dabei wurde ein digitales System konzipiert, dass eine alltagsnahe und longitudinale Erhebung ermöglicht. Im working paper wurde über alle Teilnehmenden hinweg eine Problemidentifikation der derzeitigen IST-Situation integriert, um anhand dieser Probleme und Hemmschwellen ein übergreifendes Lösungskonzept zu erarbeiten. Im Lösungsraum wurden sowohl spezifische Anforderungen seitens der Versorger als auch PatientInnen zusammengefasst und gegenübergestellt. Dabei wurde ebenfalls die Vernetzung der einzelnen Akteure untereinander beleuchtet sowie die Thematik der Datenspende angerissen.
- ItemMetadatenschema für Schulungsmaterialien zum Thema Forschungsdatenmanagement(Meyrin : CERN, 2020-04-27) Biernacka, Katarzyna; Danker, Sarah Ann; Engelhardt, Claudia; Helbig, Kerstin; Hendriks, Sonja; Jacob, Juliane; Jagusch, Gerald; Lanza, Giacomo; Leone, Claudio; Meier, Kristin; Neumann, Janna; Odebrecht, Carolin; Peters, Karsten; Rehwald, Stephanie; Rex, Jessica; Senft, Matthias; Strauch, Annette; Thiemann, Kathrin; Trautwein-Bruns, Ute; Wiljes, Cord; Wuttke, Ulrike; Ziedorn, FraukeDas Dokument enthält ein Metadatenschema für Schulungsmaterialien zum Thema Forschungsdatenmanagement. Dieses Schema wurde von der UAG Schulungen/Fortbildungen der DINI/nestor AG Forschungsdaten erstellt und bei der Materialsammlung von FDM-Schulungsmaterialien unter https://rs.cms.hu-berlin.de/uag_fdm/ umgesetzt.
- ItemDiscussion on Existing Standards and Quality Criteria in Nanosafety Research : Summary of the NanoS-QM Expert Workshop(Zenodo, 2021) Binder, Kunigunde; Bonatto Minella, Christian; Elberskirchen, Linda; Kraegeloh, Annette; Liebing, Julia; Petzold, Christiane; Razum, Matthias; Riefler, Norbert; Schins, Roel; Sofranko, Adriana; van Thriel, Christoph; Unfried, KlausThe partners of the research project NanoS-QM (Quality- and Description Standards for Nanosafety Research Data) identified and invited relevant experts from research institutions, federal agencies, and industry to evaluate the traceability of the results generated with the existing standards and quality criteria. During the discussion it emerged that numerous studies seem to be of insufficient quality for regulatory purposes or exhibit weaknesses with regard to data completeness. Deficiencies in study design could be avoided by more comprehensive use of appropriate standards, many of which already exist. The use of Electronic Laboratory Notebooks (ELNs) that allow for early collection of metadata and enrichment of datasets could be one solution to enable data re-use and simplify quality control. Generally, earlier provision and curation of data and metadata indicating their quality and completeness (e.g. guidelines, standards, standard operating procedures (SOPs) that were used) would improve their findability, accessibility, interoperability, and reusability (FAIR) in the nanosafety research field.